Application of COMPOCHIP microarray to investigate the bacterial communities of different composts

Synergetic effect and mechanism of elementary sulphur, MgSO4 and KH2PO4 progressive reinforcement on pig manure composting nitrogen retention

The potential of sulphur (S), MgSO₄ (Mg), and KH₂PO₄ (P) in nitrogen retention, ammonia emission decrease, and microbial community succession during composting needs to be investigated. To achieve this, different levels of S (0, 0.2, 0.4, 0.6, and 0.8% in dry weight) plus Mg and P (S + Mg + P) were progressively added in 70 days pig manure aerobic composting. The results revealed that the amendment increased salinity and lowered pH and dephytotoxication of the product with the increase of S amount. However, no significant inhibition effects were observed on the evolution of the thermophilic phase and product maturity. In addition, the amendment significantly reduced the total NH₃ and N₂O emissions by 29.66%-58.83% and 20.89%-56.53%, increased NH₄⁺ level by 17.31%-73.27% in thermophilic phase and NO₃^- content by 37.12%-54.84% in a mature phase, and elevated the total Kjeldahl nitrogen content by 15.49%-37.35% during the composting. In addition, compared to the control, the supplement markedly encouraged the formation of guanite in the compost product. The S addition stimulated the growth of Anseongella, Actinomadura, Chelativorans, Castellaniella, Luteimonas, and Steroidobacter microbial communities which functioned well in the degradation of nitrogen-containing compounds and organic matter. Evidence from Redundancy Analysis, Firmicutes, Myxococcus, Chloroflexi, Gemmatimonadota, and Deinococcota showed positive correlations with pH. These results imply that adding S-Mg-P amendment encourages the population and activity of specific functional microorganisms, and facilitated the ammonia emission reduction by lowering pH and thus reserved nitrogen through the formation of guanite during composting. The investigation of bacterial community abundance and environmental variables at the phylum and genus levels over time revealed that adding of 0.6% S in conjunction with P and Mg minerals was suitable for nitrogen loss mitigation in composting. The findings suggest using S + Mg + P supplement to conserve nitrogen in pig dung aerobic composting.

Effect of the lignocellulolytic Psychrotroph Lelliottia sp. on bacterial community succession in corn straw compost

This study aimed to explore the effect of an inoculation, Lelliottia sp., on the corn straw compost's physico-chemical properties, composition, and the succession of bacterial community structure. The compost community composition and succession changed after Lelliottia sp. inoculation. Inoculation increased the bacterial community diversity and abundance in the compost to promote composting. The inoculated group entered the thermophilic stage on the first day, lasting 8 days. Judging the pile maturity based on the carbon:nitrogen ratio and germination index values, the inoculated group reached the maturity standard, which was 6 days faster than the control group. The relationship between environmental factors and bacterial communities was comprehensively analyzed using redundancy analysis. Temperature and carbon:nitrogen ratio were the main environmental factors driving the succession of bacterial communities, to provide basic information on the changes of physicochemical indexes and bacterial community succession in Lelliottia sp. inoculated maize straw composting, providing assistance for practical composting applications of this strain.

Valorizing kitchen waste to produce value-added fertilizer by thermophilic semi-continuous composting followed by static stacking: Performance and bacterial community succession analysis

To explore an effective decentralized kitchen waste (KW) treatment system, the performance and bacterial community succession of thermophilic semi-continuous composting (TSC) of KW followed by static stacking (SS) was studied. A daily feeding ratio of 10% ensured stable performance of TSC using an integrated automatic reactor; the efficiencies of organic matter degradation and seed germination index (GI) reached 80.88% and 78.51%, respectively. SS for seven days further promoted the quality of the compost by improving the GI to 91.58%. Alpha- and beta-diversity analyses revealed significant differences between the bacterial communities of TSC and SS. Firmicutes, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Myxococcota were dominant during the TSC of KW, whereas the members of Proteobacteria and Bacteroidetes responsible for product maturity rapidly proliferated during the subsequent SS and ultimately dominated the compost with Firmicutes and Actinobacteria. These results provide new perspectives for decentralized KW treatment using TSC for practical applications.

Composting pig manure with nano-zero-valent iron amendment: Insights into the carbon cycle and balance

The effectiveness of nano-zero-valent-iron (NZVI) addition during composting of pig manure (PM) was investigated. Different dosages of NZVI were mixed with PM substrate during a 50 days composting process. The results revealed that the higher share of NZVI addition, the higher OM degradation rate is. On contrary, it was observed that the higher share of NZVI addition, the lower the fulvic acid and the humin degradation rate is. Meanwhile, NZVI amendment increased the CO₂ and CH₄ emissions by 29-47 % and 53-57 %, respectively. The in-depth analysis showed that NZVI addition increased the activity of Sphaerobacter and Luteimonas, which eventually led to the degradation of hard-to-degrade OM faster. Additionally, NZVI was found to increase the filtration of microorganisms, reducing the toxicity and hygiene of compost products. No significant improvement in humic substance enhancement was observed during composting with NZVI addition but improved OM degradation.

Bacterial Community Drives the Carbon Source Degradation during the Composting of Cinnamomum camphora Leaf Industrial Extracted Residues

The increasing production of industrial aromatic plant residues (IAPRs) are potentially environmental risky, and composting is a promising solution to resolve the coming IAPR problems. Carbon source degradation is a basic but important field in compost research; however, we still lack a clear understanding of carbon source degradation and the corresponding relationship to microbial community variation during IAPR composting, which hampers the improvement of IAPR composting efficiency and the promotion of this technology. In this study, samples were chosen on the first day, the 10th day, the 20th day, and the last day during the composting of Cinnamomum camphora leaf IAPRs, and the microbial community composition, main carbon source composition, and several enzyme activities were measured accordingly. The results showed that during composting, the hemicellulose had the highest reduction (200 g kg−1), followed by cellulose (143 g kg−1), lignin (15.5 g kg−1), starch (5.48 g kg−1), and soluble sugar (0.56 g kg−1), which supported that hemicellulose and cellulose were the main carbon source to microbes during composting. The relative abundance of the main bacterial phylum Firmicute decreased from 85.1% to 40.3% while Actinobactreia increased from 14.4% to 36.7%, and the relative abundance of main fungal class Eurotiomycetes decreased from 60.9% to 19.6% while Sordariomycetes increased from 16.9% to 69.7%. Though principal coordinates analysis found that both bacterial and fungal community composition significantly varied during composting (p < 0.05), structure equation modeling (SEM) supported that bacterial composition rather than fungal counterpart was more responsible for the change in carbon source composition, as the standard total effects offered by bacterial composition (−0.768) was about five times the fungal composition (−0.144). Enzyme2 (comprised of xylanase, laccase, cellulase and manganese peroxidase) provided −0.801 standard total effects to carbon source composition, while Enzyme1 (comprised of lignin peroxidase and polyphenol oxidase) had only 0.172. Furthermore, xylanase and laccase were the only two enzymes appeared in co-occurrence network, clustered with nearly all the carbon sources concerned (except starch) in module-II. Xylanase, hemicellulose, and cellulose were linked to higher numbers of OTUs, more than laccase and other carbon sources. In addition, there were 11 BOTUs but only 1 FOTUs directly interacted to xylanase, hemicellulose, and cellulose simultaneously, three of them were Limnochordaceae and two were Savagea, which highlighted the potential core function in lignocellulose degradation provided by bacterial members, especially Limnochordaceae and Savagea. Thus, the results supported that during composting of Cinnamomum camphora leaf IAPRs, the degradation of dominate carbon sources, hemicellulose and cellulose, was mainly driven by bacterial community rather than fungal community. In addition, the bacterial originated xylanase and laccase played potentially core roles in the functional modules. This research clearly investigated the microbial dynamics of carbon source degradation during the composting of Cinnamomum camphora leaf IAPRs, and offers valuable information about and new insight into future IAPRs waste treatment.

Phytotoxicity of farm livestock manures in facultative heap composting using the seed germination index as indicator

Static facultative heap composting of animal manure is widely used in China, but there is almost no systematic research on the phytotoxicity of the produced compost. Here, we evaluated the phytotoxic variation in compost produced by facultative heap composting of four types of animal manure (chicken manure, pig manure, sheep manure, and cattle manure) using different plant seeds (cucumber, radish, Chinese cabbage, and oilseed rape) to determine germination index (GI). The key factors that affected GI values were identified, including the dynamics of the phytotoxicity and microbial community during heap composting. Sensitivity to toxicity differed depending on the type of plant seed used. Phytotoxicity during facultative heap composting, evaluated by the GI, was in the order: chicken manure (0-6.6 %) < pig manure (14.4-90.5 %) < sheep manure (46.0-93.0 %) < cattle manure (50.2-105.8 %). Network analysis showed that the volatile fatty acid (VFA) concentration was positively correlated with Firmicutes abundance, and NH₄⁺-N was correlated with Actinobacteria, Proteobacteria, and Bacteroidetes. More bacteria were stimulated to participate in conversions of dissolved organic carbon, dissolved nitrogen, VFA, and ammonia-nitrogen (NH₄⁺-N) in sheep manure heap composting than that in other manure. The GI was most affected by VFA in chicken manure and cattle manure heap composting, while NH₄⁺-N was the main factor affecting the GI in pig manure and sheep manure compost. The dissolved carbon and nitrogen content and composition, as well as the core and proprietary microbial communities, were the primary factors that affected the succession of phytotoxic substances in facultative heap composting, which in turn affected GI values. In this study, the key pathways of livestock manure composting that affected GI and phytotoxicity were found and evaluated, which provided new insights and theoretical support for the safe use of organic fertilizer.

Biochar improved the composting quality of seaweeds and cow manure mixture and altered the microbial community

The beneficial effects of biochar addition during composting have been proved for many feedstocks, like manures and crop straws. However, the effect of biochar on the quality of composting product with seaweed as the feedstock and the bacterial response has not been investigated. In this study, the wheat straw biochar addition on the quality of the composting product and the bacterial response was explored at the rate of 0-10%. The results showed that biochar addition at the optimal rate (5%, w/w) could increase the germination index and the ratio of the optical density of humic acid at 460 nm to that at 660 nm (E4/E6) of the composting product, which indicated the decreased biotoxicity and enhanced compost maturity. The significant increase of the nitrate nitrogen (NO₃ ^--N) content of the composting product proved the improvement of N cycling during composting process with biochar addition. The bacterial community of composting product was shifted and the relative abundance of some beneficial taxa (e.g., Muricauda and Woeseia) was significantly increased with biochar addition. Furthermore, the relative abundance of some bacterial genes related to amino acid metabolism and carbohydrate metabolism was also increased with biochar addition. The results of our study provided the positive effect of biochar addition on the composting of seaweed and could help to produce high quality seaweed fertilizer by composting with biochar addition.

Effect of moisture content on the evolution of bacterial communities and organic matter degradation during bioaugmented biogas residues composting

Composting is an excellent way to recycle biogas residues into a stable, non-toxic agricultural end product. In this study, the dynamic changes of physical-chemical parameters and bacterial community in three groups of bioaugmentation composting systems at different moisture contents (MC) of 50% (MC50), 60% (MC60) and 70% (MC70) were monitored. The differences of bacterial communities in composts with different initial MC were compared, and the interaction between biological and non-biological parameters was also explored. The results revealed that after 30 days of composting, the biogas residues compost in MC60 reached highest temperature of 64 °C, total Kjeldahl nitrogen (TKN) of 2%, seed germination index (GI) of 110%, and the longest thermophilic period duration of 5 days (55 °C). Additionally, the result of high-throughput sequencing showed that the diversity of bacterial communities in MC60 was the highest, and the abundance of Actinobacteria (16.93-52.63%), Firmicutes (8.71-56.75%), and Proteobacteria (16.88-46.95%) in all groups were the highest at phylum level. The LEfSe analysis indicated that the abundance of Ochrobactrum and Cellulomonadaceae in MC60 was significantly (p < 0.05) higher than with other treatments. Moreover, canonical correspondence analysis (CCA) indicated thermophilic period duration is significantly (p < 0.05) positively correlated with Paenibacillus. Besides, it was found the relative abundance of Nocardiopsis and Georgenia has a significant (p < 0.01) correlation with the fertilizer efficiency of compost. These results showed that controlling the initial moisture content at 60% can improve the maturity and fertilizer efficiency of compost, and enable the bacteria beneficial to composting to gain the advantage of proliferation.

Use of activated carbon to reduce ammonia emissions and accelerate humification in composting digestate from food waste

Management of digestate from food waste (DFW) is becoming the bottleneck of the food waste anaerobic digestion. Composting is a feasible method to dispose the DFW and convert it to organic fertilizer; however, high ammonia (NH₃) emissions and long composting time are key concerns in this process. In this study, the mechanism of activated carbon (AC) on the loss of NH₃ and humification during DFW composting was investigated. The use of AC could promote humification, shorten 50% of the DFW composting period, and decrease the NH₃ emissions by 34%. Results of the microbial analysis indicated that the AC could promote the growth of key microbes (i.e., Wallemia genus for fungi; and Fastidiosipila genus for bacteria). The Cladosporium and Fastidiosipila genera developed in the fractions closely and loosely attached to the AC, respectively, leading to faster degradation of lignocellulose matter. In addition, AC could enrich the Ammoniibacillus genus, reducing nitrogen loss.

Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.

Bacterial Succession during Vermicomposting of Silver Wattle (Acacia dealbata Link)

Vermicomposting is the process of organic waste degradation through interactions between earthworms and microbes. A variety of organic wastes can be vermicomposted, producing a nutrient-rich final product that can be used as a soil biofertilizer. Giving the prolific invasive nature of the Australian silver wattle Acacia dealbata Link in Europe, it is important to find alternatives for its sustainable use. However, optimization of vermicomposting needs further comprehension of the fundamental microbial processes. Here, we characterized bacterial succession during the vermicomposting of silver wattle during 56 days using the earthworm species Eisenia andrei. We observed significant differences in α- and β-diversity between fresh silver wattle (day 0) and days 14 and 28, while the bacterial community seemed more stable between days 28 and 56. Accordingly, during the first 28 days, a higher number of taxa experienced significant changes in relative abundance. A microbiome core composed of 10 amplicon sequence variants was identified during the vermicomposting of silver wattle (days 14 to 56). Finally, predicted functional profiles of genes involved in cellulose metabolism, nitrification, and salicylic acid also changed significantly during vermicomposting. This study, hence, provides detailed insights of the bacterial succession occurring during vermicomposting of the silver wattle and the characteristics of its final product as a sustainable plant biofertilizer.

Two types nitrogen source supply adjusted interaction patterns of bacterial community to affect humifaction process of rice straw composting

This study investigated effects of high-nitrogen source (urea) (R_UR) and protein-like nitrogen source (chicken manure) (R_CM) on humification process during lignocellulose biomass composting. It demonstrated that decreasing ratio of crude fiber (CF), polysaccharide (PS) and amino acids (AAs) in R_CM (29.75%, 53.93% and 73.73%, respectively) was higher than that in R_UR (14.73%, 28.74% and 51.92%, respectively). Humic substance (HS) concentration increased by 7.51% and 73.05% during R_UR and R_CM composting, respectively. The lower total links, more independent modularization and higher proportion of positive correlations between functional bacteria and organic components was observed with R_CM network than R_UR, indicating that protein-like nitrogen source supply may alleviate competition within bacterial community. Moreover, chicken manure supply favorably selects greater special functional bacterial taxa (Pusillimonas, Pedomicrobium, Romboustia and other 24 genus) related to AAs and stimulates the collaborative division of bacterial community. This is significance for strengthening effective transformation of organic components.

Revisiting the succession of microbial populations throughout composting: A matter of thermotolerance

Composting has been traditionally considered a process in which a succession of mesophilic and thermophilic microbial populations occurs due to temperature changes. In order to deepen in this model, 1380 bacterial and fungal strains (the entire culturable microbiota isolated from a composting process) were investigated for their ability to grow across a wide range of temperatures (20 to 60 °C). First, qualitative tests were performed to establish a thermal profile for each strain. Then, quantitative tests allowed ascertaining the extent of growth for each strain at each of the tested temperatures. The identity of the isolates enabled to position them taxonomically and permitted tracking the strains throughout the process. Results showed that 90% of the isolates were classified as thermotolerant (they grew at all tested temperatures). Only 9% and 1% of the studied strains showed to be strictly mesophilic or thermophilic, respectively. Firmicutes exhibited the greatest thermal plasticity, followed by Actinobacteria and Ascomycota. Most of the Proteobacteria and all Basidiomycota strains were also able to grow at all the assayed temperatures. Thermotolerance was clearly demonstrated among the composting microbiota, suggesting that the idea of the succession of mesophilic and thermophilic populations throughout the process might need a reassessment.

The degradation of organic matter coupled with the functional characteristics of microbial community during composting with different surfactants

The purpose of this study was to investigate the effects of anionic and cationic surfactants on the physico-chemical properties, organic matter (OM) degradation, bacterial community structure and metabolic function during composting of dairy manure and sugarcane bagasse. The results showed that the surfactant could optimize the composting conditions to promote the degradation of OM. The most OM degradation and humic substances (HS) synthesis were observed in SAS. Firmicutes and Proteobacteria were more abundant in SAS and CTAC, and Actinobacteria in CK. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that SAS and CTAC are more abundant than CK in genes related to metabolism, environmental and genetic information processing. The correlation analysis showed that the dominant bacteria had more significant correlation with environmental factors. In general, the anionic surfactant could better promote the degradation of OM, change the structure of microbial community, and improve the quality of compost.

Roles of non-ionic surfactant sucrose ester on the conversion of organic matters and bacterial community structure during composting

The purpose of this study was to investigate the effect of sucrose ester (SE) addition on the physico-chemical parameters, organic matter (OM) biodegradation and related bacterial communities structure in dairy manure and cassava residuals co-composting. The biodegradation rates of OM, dissolved organic matters (DOM) and lignocellulose in SE (16.34%, 44.11% and 26.73%) group were higher than those in CK (14.71%, 39.11% and 19.90%). In addition, the content of humic substances (HS) (36.34%) in SE was obviously higher than that in CK (17.68%). The relative abundance of bacterial community in SE changed, in which the abundance of Firmicutes and Actinobacteria increased, while the amount of Blastomonas decreased. Redundancy analysis indicated Bacillus and Acinetobacter were positively correlated with the temperature and OM, whereas Azomonas and Luteimonas showed a positive relation with pH. In conclusion, the amendment of SE accelerated the degradation and conversion of organic matters, enhanced the formation of HS and improved the quality of compost.

Food Waste Composting and Microbial Community Structure Profiling

Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

Microbial community composition, co-occurrence network pattern and nitrogen transformation genera response to biochar addition in cattle manure-maize straw composting

A better understanding of the microbial group influencing nitrogen (N) dynamics and cycling in composting matrix is critical in achieving good management to alleviate N loss and improve final compost quality. This study investigated the bacterial composition, structure, co-occurrence network patterns and topological roles of N transformation in cattle manure-maize straw composting using high-throughput sequencing. The two treatments used in this experiment were cattle manure and maize straw mixture (CM) and CM with 10% biochar addition (CMB). In both treatments, the bacterial community composition varied during composting and the major phyla included Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes and Chloroflexi. The phyla Actinobacteria and Proteobacteria were more abundant in CMB treatment while Firmicutes was abundant in CM piles. The metabolic functional profiles of bacteria was predicted using the "phylogenetic investigation of communities by reconstruction of unobserved states" (PICRUSt) which revealed that except for cellular processes pathway, CMB had slight higher abundance in metabolism, genetic information processing and environmental information processing than the CM. Pearson correlation revealed more significant relationship between the important bacteria communities and N transformation in CMB piles compared with CM. Furthermore, network pattern analysis revealed that the bacterial networks in biochar amended piles are more complex and harbored more positive links than that of no biochar piles. Corresponding agreement of multivariate analyses (correlation heatmap, stepwise regression, Path and network analyses) revealed that Psychrobacter, Thermopolyspora and Thermobifida in CM while Corynebacterium_1, Thermomonospora and Streptomyces in CMB were key bacterial genera affecting NH₄⁺-N, NO₃^--N and total nitrogen (TN) transformation respectively during composting process. These results provide insight into nitrogen transformation and co-occurrence patterns mediating microbes and bacterial metabolism which could be useful in enhancing compost quality and mitigating N loss during composting.

The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets

An organism’s gut microbiome handles most of the metabolic processes associated with food intake and digestion but can also strongly affect health and behavior. A stable microbial core community in the gut provides general metabolic competences for substrate degradation and is robust against extrinsic disturbances like changing diets or pathogens. Black Soldier Fly larvae (BSFL; Hermetia illucens) are well known for their ability to efficiently degrade a wide spectrum of organic materials. The ingested substrates build up the high fat and protein content in their bodies that make the larvae interesting for the animal feedstuff industry. In this study, we subjected BSFL to three distinct types of diets carrying a low bioburden and assessed the diets’ impact on larval development and on the composition of the bacterial and archaeal gut community. No significant impact on the gut microbiome across treatments pointed us to the presence of a predominant core community backed by a diverse spectrum of low-abundance taxa. Actinomyces spp., Dysgonomonas spp., and Enterococcus spp. as main members of this community provide various functional and metabolic skills that could be crucial for the thriving of BSFL in various environments. This indicates that the type of diet could play a lesser role in guts of BSFL than previously assumed and that instead a stable autochthonous collection of bacteria provides the tools for degrading of a broad range of substrates. Characterizing the interplay between the core gut microbiome and BSFL helps to understand the involved degradation processes and could contribute to further improving large-scale BSFL rearing.

Effect of thermotolerant bacterial inoculation on the microbial community during sludge composting

A thermophilic bacterium (Geobacillus stearothermophilus CHB1) was inoculated in a sludge compost, and the effects of the inoculation on the abundance and structure of the bacterial community in the sludge compost were investigated using quantitative PCR and Illumina MiSeq sequencing. The results showed that the high-temperature stage (>50 °C) of the CHB1 and CK (control without inoculum) piles started on days 5 and 8, respectively, and lasted for 7 and 2 days, respectively, indicating the extension of the thermophilic phase by CHB1 inoculation in the sludge compost. At the end of composting, the CHB1 piles showed a higher loss of total organic carbon, lower C/N ratio, and lower moisture content. The abundance of bacteria in the CHB1 piles was significantly higher in the heating and thermophilic phase of composting but were lower than those of the CK in the cooling phase. The richness and diversity of the bacterial community in the thermophilic phase increased after inoculation with CHB1. After inoculation of CHB1, there were higher relative abundances of Firmicutes, Thermopolyspora, Thermobacillus, Thermomonas, Thermomonospora, and Thermovum, which can grow in a high-temperature environment. Furthermore, redundancy analysis indicated that total organic carbon, total nitrogen, C/N ratio, pH, temperature, and moisture were the significant parameters that affected the bacterial community structure during sludge composting. Our findings suggested that inoculation with CHB1 would enhance the quality and efficiency of composting.

Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost

Vermicomposting is the process by which organic waste is broken down through the synergistic actions of earthworms and microbial communities. Although vermicomposting has been shown to effectively reduce organic biomass and generate high-quality fertilizer for plants, little is known about the bacterial communities that are involved in this decomposition process. Since optimization of vermicomposting for commercial use necessitates additional knowledge of the underlying biological processes, this study sought to characterize the bacterial succession involved in the vermicomposting of Scotch broom (Cytisus scoparius), a leguminous shrub that has become invasive around the world with consequences for the dynamics and productivity of the ecosystems they occupy. Scotch broom was processed in a pilot-scale vermireactor for 91 days with the earthworm species Eisenia andrei. Samples were taken at the initiation of vermicomposting, and days 14, 42 and 91, representing both active and mature stages of vermicomposting. Significant changes (P < 0.0001) in the bacterial community composition (richness and evenness) were observed throughout the process. Increases in taxonomic diversity were accompanied by increases in functional diversity of the bacterial community, including metabolic capacity, streptomycin and salicylic acid synthesis, and nitrification. These results highlight the role of bacterial succession during the vermicomposting process and provide evidence of microbial functions that may explain the beneficial effects of vermicompost on soil and plants.

Manipulation of the rhizosphere bacterial community by biofertilizers is associated with mitigation of cadmium phytotoxicity

The objective of this study was to understand the effect of biofertilizers on cadmium (Cd)-induced phytotoxicity and the rhizosphere bacterial community. The crop specie rice (Oryza sativa L.) was planted in Cd-contaminated soils, and Illumina high-throughput sequencing was performed to investigate how the composition of the rhizosphere bacterial community responded to the addition of biofertilizers. Biofertilizers were effective in alleviating Cd phytotoxicity as indicated by the significant increase in plant biomass (up to 85.2% and 48.4% for roots and shoots, respectively) and decrease in tissue Cd concentration (up to 72.2% in roots) of rice receiving fertilizer treatments compared with the CK (no treatment). These positive effects were likely due to the increase in soil pH, which can be attributed primarily to Cd immobilization, and the promotion of beneficial taxa such as Proteobacteria, Bacteroidetes, Gemmatimonadetes, and Firmicutes. In addition, autoclaved biofertilizers tended to have similar beneficial effects and similar bacterial community alpha diversities as the original biofertilizer treatments. This suggests that the change in soil physicochemical properties by biofertilizer addition might drive the structure of rhizosphere bacterial community, and not the biofertilizer microbes themselves. In both the original and sterilized biofertilizer treatments, the effectiveness in mitigating of Cd phytotoxicity was found to be dependent on the type of biofertilizer applied. Comparatively, the biofertilizer denoted as DY was more effective in mitigating Cd phytotoxicity than others. These results demonstrate that biofertilizer addition could be a promising approach to immobilize soil Cd by manipulating the rhizosphere bacterial community, thus to facilitate plant growth.

Fluorescence-switching RNA for detection of bacterial ribosomes

We have developed an efficient chemical system that allows quantification of bacterial ribosomes by fluorescence-based analysis. The key component in the system is the exciton-controlled fluorescent RNA aptamer, which recognizes neomycin B. The intensity of fluorescence from such a ribosome-sensing system increased drastically in the presence of Escherichia coli.

Benefits to decomposition rates when using digestate as compost co-feedstock: Part II - Focus on microbial community dynamics

Linkage between composting reactor performance and microbial community dynamics was investigated during co-composting of digestate and fresh feedstock (organic fraction of municipal solid waste) using 25L reactors. Previously, the relationship between composting performance and various physicochemical parameters were reported in Part I of the study (Arab and McCartney, 2017). Three digestate to fresh feedstock ratios (0, 40, and 100%; wet weight basis) were selected for analysis of microbial community dynamics. The 40% ratio was selected because it was found to perform the best (Arab and McCartney, 2017). Illumina sequencing results revealed that the reactor with a greater composting performance (higher organic matter degradation and higher heat generation; 40% ratio) was associated with higher microbial diversity. Two specific bacterial orders that might result in higher performance were Thermoactinomycetaceae and Actinomycetales with a higher sequence abundance during thermophilic composting phase and during the maturing composting phase, respectively. Galactomyces, Pichia, Chaetomium, and Acremonium were the four fungal genera that are probably also involved in higher organic matter degradation in the reactor with better performance. The redundancy analysis (RDA) biplot indicated that among the studied environmental variables, temperature, total ammonia nitrogen and nitrate concentration accounted for much of the major shifts in microbial sequence abundance during the co-composting process.

Bacterial community structure transformed after thermophilically composting human waste in Haiti

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible.

Chestnut green waste composting for sustainable forest management: Microbiota dynamics and impact on plant disease control

Making compost from chestnut lignocellulosic waste is a possible sustainable management strategy for forests that employs a high-quality renewable organic resource. Characterization of the microbiota involved in composting is essential to better understand the entire process as well as the properties of the final product. Therefore, this study investigated the microbial communities involved in the composting of chestnut residues obtained from tree cleaning and pruning. The culture-independent approach taken highlighted the fact that the microbiota varied only slightly during the process, with the exception of those of the starting substrate and mature compost. The statistical analysis indicated that most of the bacterial and fungal species in the chestnut compost persisted during composting. The dominant microbial population detected during the process belonged to genera known to degrade recalcitrant lignocellulosic materials. Specifically, we identified fungal genera, such as Penicillium, Fusarium, Cladosporium, Aspergillus and Mucor, and prokaryotic species affiliated with Bacilli, Actinobacteria, Flavobacteria and γ-Proteobacteria. The suppressive properties of compost supplements for the biocontrol of Sclerotinia minor and Rhizoctonia solani were also investigated. Compared to pure substrate, the addition of compost to the peat-based growth substrates resulted in a significant reduction of disease in tomato plants of up to 70 % or 51 % in the presence of Sclerotinia minor or Rhizoctonia solani, respectively. The obtained results were related to the presence of putative bio-control agents and plant growth-promoting rhizobacteria belonging to the genera Azotobacter, Pseudomonas, Stenotrophomonas, Bacillus, Flavobacterium, Streptomyces and Actinomyces in the chestnut compost. The composting of chestnut waste may represent a sustainable agricultural practice for disposing of lignocellulosic waste by transforming it into green waste compost that can be used to improve the fitness of agricultural plants.

Co-composting of biowaste and wood ash, influence on a microbially driven-process

A trial at semi-industrial scale was conducted to evaluate the effect of wood ash amendment on communal biowaste in a composting process and on the final composts produced. For this purpose, three treatments including an unamended control (C0) and composts with additions of 6% (C6), and 12% (C12) of wood ash (w/w) were studied, and physico-chemical parameters as well as microbial activity and community composition were investigated. At the end of the process, composts were tested for toxicity and quality, and microbial physiological activity. The influence of ash addition on compost temperature, pH, microbial activity and composition was stronger during the early composting stages and diminished with time, whereby composts became more similar. Using the COMPOCHIP microarray, a reduction in the pathogenic genera Listeria and Clostridium was observed, which together with the temperature increases of the composting process helped in the hygienisation of composts. Lactobacillus species were also affected, such that reduced hybridisation signals were observed with increased ash addition, due to the increased pH values in amended composts. Organic matter mineralisation was also increased through ash addition, and no negative effects on the composting process were observed. The nutrient content of the final products was increased through the addition of ash, and no toxic effects were observed. Nonetheless, greater concentrations of heavy metals were found in composts amended with more ash, which resulted in a downgrading of the compost quality according to the Austrian Compost Ordinance. Thus, regulation of both input materials and end-product quality is essential in optimising composting processes.

Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant

Composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. We employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. The investigation of microbial succession revealed that Bacillales, Actinobacteria and Saccharomyces increased significantly with respect to abundance in composting process. The key microbiologic population for cellulose degradation in different composting stages was different. Fungi were found to be the main producers of cellulase in earlier phase. However, the cellulolytic fungal communities were gradually replaced by a purely bacterial one in active phase, which did not support the concept that the thermophilic fungi are active through the thermophilic phase. The effective decomposition of cellulose required the synergy between bacteria and fungi in the curing phase.

High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control

Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

Compost: its role, mechanism and impact on reducing soil-borne plant diseases

Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.

Coffee husk composting: an investigation of the process using molecular and non-molecular tools

Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts.

Changes in the microbial communities during co-composting of digestates

Anaerobic digestion is a waste treatment method which is of increasing interest worldwide. At the end of the process, a digestate remains, which can gain added value by being composted. A study was conducted in order to investigate microbial community dynamics during the composting process of a mixture of anaerobic digestate (derived from the anaerobic digestion of municipal food waste), green wastes and a screened compost (green waste/kitchen waste compost), using the COMPOCHIP microarray. The composting process showed a typical temperature development, and the highest degradation rates occurred during the first 14 days of composting, as seen from the elevated CO2 content in the exhaust air. With an exception of elevated nitrite and nitrate levels in the day 34 samples, physical-chemical parameters for all compost samples collected during the 63 day process indicated typical composting conditions. The microbial communities changed over the 63 days of composting. According to principal component analysis of the COMPOCHIP microarray results, compost samples from the start of the experiment were found to cluster most closely with the digestate and screened compost samples. The green waste samples were found to group separately. All starting materials investigated were found to yield fewer and lower signals when compared to the samples collected during the composting experiment.

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Assessment of bacterial diversity during composting of agricultural byproducts

Background

Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts.

Results

The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 10⁵ to 10⁹ cfu g^-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts.

Conclusion

The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost. These bacteria can be used as potential compost inoculants for accelerating composting process.

Archaeal community dynamics and abiotic characteristics in a mesophilic anaerobic co-digestion process treating fruit and vegetable processing waste sludge with chopped fresh artichoke waste

This study evaluated the feasibility of obtaining methane in anaerobic digestion (AD) from the waste products generated by the processing of fruit and vegetables. During the first phase (0-55 d) of the AD using sludge from fruit and vegetable processing, an average value of 244±88 L kg(-1) dry matter d(-1)of biogas production was obtained, and methane content reached 65% of the biogas. Co-digestion with chopped fresh artichoke wastes in a second phase (55-71 d) enhanced biogas production, and resulted in an average value of 354±68 L kg(-1) dry matter d(-1), with higher methane content (more than 70%). The archaeal community involved in methane production was studied using the ANAEROCHIP microarray and real-time PCR. Results indicated that species of Methanosaeta and Methanosarcina were important during the AD process. Methanosarcina numbers increased after the addition of chopped fresh artichoke, while Methanosaeta numbers decreased.

Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.

Effects of pH and microbial composition on odour in food waste composting

A major problem for composting plants is odour emission. Slow decomposition during prolonged low-pH conditions is a frequent process problem in food waste composting. The aim was to investigate correlations between low pH, odour and microbial composition during food waste composting. Samples from laboratory composting experiments and two large scale composting plants were analysed for odour by olfactometry, as well as physico-chemical and microbial composition. There was large variation in odour, and samples clustered in two groups, one with low odour and high pH (above 6.5), the other with high odour and low pH (below 6.0). The low-odour samples were significantly drier, had lower nitrate and TVOC concentrations and no detectable organic acids. Samples of both groups were dominated by Bacillales or Actinobacteria, organisms which are often indicative of well-functioning composting processes, but the high-odour group DNA sequences were similar to those of anaerobic or facultatively anaerobic species, not to typical thermophilic composting species. High-odour samples also contained Lactobacteria and Clostridia, known to produce odorous substances. A proposed odour reduction strategy is to rapidly overcome the low pH phase, through high initial aeration rates and the use of additives such as recycled compost.

An optimized DNA extraction and purification method from dairy manure compost for genetic diversity analysis

An unbiased DNA extraction protocol is necessary for analysis of genetic diversity, particularly, of genes in complex environmental samples by nucleic acid techniques. In the present study, three manual extraction methods and two commonly used commercial kits, which were accompanied by two DNA purification strategies, were compared based on cell lysis efficiency, DNA and humic acid yields, PCR amplification and denaturing gradient gel electrophoresis (DGGE) analysis. The results show that in spite of higher cell lysis efficiencies of the two commercial kits, the purified DNA yields were only one-third of that obtained by the two manual methods of FTSP (Freeze-thaw-SDS-Protein K) and FTSPP (Freeze-thaw-SDS-Protein K-Polyvinylpolypyrrolidone). The purified DNA from all five methods was pure enough for successful PCR and real-time PCR amplifications in the presence of 1 μg μL(-1) BSA. However, the FTSPP extraction method with DNA purification by a Wizard(®) kit yielded the largest number of 16S rRNA gene copies and ribotypes or bands in DGGE profiles, which indicated a superiority over the other four methods. The development of this optimized DNA extraction and purification method may provide a valuable tool for further molecular analysis of compost.

Development of bacteria identification array to detect lactobacilli in Thai fermented sausage

To improve the quality and safety of food products, there is a need in the food industry for a reliable method for simultaneously monitoring multiple bacterial strains. Microarray technology is a high-throughput screening approach that can provide an alternative for bacteria detection. A total of 164 bacteria-specific probes were designed from 16S rRNA gene sequences to target 12 bacteria species, including lactic acid bacteria and selected food pathogens. After fabrication onto aminosilane-coated slides, hybridization conditions of the array were optimized for high specificity and signal intensities. The array was applied to detect 12 bacteria individually and was specific to all (Lactobacillus plantarum group, L. fermentum, L. brevis, L. delbrueckii, L. casei, L. sakei, Escherichia coli, Staphylococcus aureus, Micrococcus luteus and Listeria monocytogenes) except L. animalis. Multiplex detection using mixed bacteria populations was evaluated and accurate detection was obtained. The feasibility of using the array to detect the target bacteria in food was evaluated with Thai fermented sausages (Nham). Meat samples were collected on days 2, 3 and 7 after natural fermentation, L. plantarum-inoculated fermentation and L. brevis-inoculated fermentation before applying to the array. The naturally-fermented Nham contained L. sakei, L. delbrueckii, L. plantarum and L. fermentum. The L. plantarum-inoculated Nham showed a similar lactic acid bacteria population but the positive signal level for L. plantarum was higher than with natural fermentation. The L. brevis-inoculated Nham contained L. brevis, L. plantarum, L. delbrueckii and L. fermentum. The array was used to monitor bacteria population dynamics during the fermentation process. The naturally-fermented and L. brevis-inoculated samples showed lower positive signal levels of L. plantarum on day 2, but signals gradually increased on days 3 and 7 of the fermentation. In contrast, the L. plantarum-started fermentation showed a higher positive signal level on day 2 than the natural and L. brevis-inoculated samples, and the positive signal level remained high on days 3 and 7. The bacteria identification array was proven to be useful as an alternative method to detect and monitor target bacteria populations during food fermentation.

Acetate activation in Methanosaeta thermophila: characterization of the key enzymes pyrophosphatase and acetyl-CoA synthetase

The thermophilic methanogen Methanosaeta thermophila uses acetate as sole substrate for methanogenesis. It was proposed that the acetate activation reaction that is needed to feed acetate into the methanogenic pathway requires the hydrolysis of two ATP, whereas the acetate activation reaction in Methanosarcina sp. is known to require only one ATP. As these organisms live at the thermodynamic limit that sustains life, the acetate activation reaction in Mt. thermophila seems too costly and was thus reevaluated. It was found that of the putative acetate activation enzymes one gene encoding an AMP-forming acetyl-CoA synthetase was highly expressed. The corresponding enzyme was purified and characterized in detail. It catalyzed the ATP-dependent formation of acetyl-CoA, AMP, and pyrophosphate (PP_i) and was only moderately inhibited by PP_i. The breakdown of PP_i was performed by a soluble pyrophosphatase. This enzyme was also purified and characterized. The pyrophosphatase hydrolyzed the major part of PP_i (K_M = 0.27 ± 0.05 mM) that was produced in the acetate activation reaction. Activity was not inhibited by nucleotides or PP_i. However, it cannot be excluded that other PP_i-dependent enzymes take advantage of the remaining PP_i and contribute to the energy balance of the cell.

Microbiological community analysis of vermicompost tea and its influence on the growth of vegetables and cereals

Vermicompost, the digestion product of organic material by earthworms, has been widely reported to have a more positive effect on plant growth and plant health than conventional compost. A study was conducted to investigate the effects of different vermicompost elutriates (aerated compost teas) on soils and plant growth. The teas were analyzed by chemical, microbiological, and molecular methods accompanied by plant growth tests at laboratory and field scale. The number of microorganisms in the teas increased during the extraction process and was affected by substrate addition. The vermicompost tea found to increase plant growth best under laboratory tests was applied to cereals (wheat and barley) and vegetables ( Raphanus sativus , Rucola selvatica , and Pisum sativum ) in a field study. The results revealed no effects of tea application on plant yield; however, sensoric tests indicated an improvement in crop quality. The soils from laboratory and field studies were investigated to detect possible microbial or chemical changes. The results indicated that minor changes to the soil microbial community occurred following tea application by foliar spray in both the laboratory-scale and field-scale experiments.

Treatment alternatives of slaughterhouse wastes, and their effect on the inactivation of different pathogens: a review

Slaughterhouse wastes are a potential reservoir of bacterial, viral, prion and parasitic pathogens, capable of infecting both animals and humans. A quick, cost effective and safe disposal method is thus essential in order to reduce the risk of disease following animal slaughter. Different methods for the disposal of such wastes exist, including composting, anaerobic digestion (AD), alkaline hydrolysis (AH), rendering, incineration and burning. Composting is a disposal method that allows a recycling of the slaughterhouse waste nutrients back into the earth. The high fat and protein content of slaughterhouse wastes mean however, that such wastes are an excellent substrate for AD processes, resulting in both the disposal of wastes, a recycling of nutrients (soil amendment with sludge), and in methane production. Concerns exist as to whether AD and composting processes can inactivate pathogens. In contrast, AH is capable of the inactivation of almost all known microorganisms. This review was conducted in order to compare three different methods of slaughterhouse waste disposal, as regards to their ability to inactivate various microbial pathogens. The intention was to investigate whether AD could be used for waste disposal (either alone, or in combination with another process) such that both energy can be obtained and potentially hazardous materials be disposed of.

Effects of continuous thermophilic composting (CTC) on bacterial community in the active composting process

The method of continuous thermophilic composting (CTC) remarkably shortened the active composting cycle and enhanced the compost stability. Effects of CTC on the quantities of bacteria, with a comparison to the traditional composting (TC) method, were explored by plate count with incubation at 30, 40 and 50°C, respectively, and by quantitative PCR targeting the universal bacterial 16S rRNA genes and the Bacillus 16S rRNA genes. The comparison of cultivatable or uncultivatable bacterial numbers indicated that CTC might have increased the biomass of bacteria, especially Bacillus spp., during the composting. Denaturing gradient gel electrophoresis (DGGE) analysis was employed to investigate the effects of CTC on bacterial diversity, and a community dominated by fewer species was detected in a typical CTC run. The analysis of sequence and phylogeny based on DGGE indicated that the continuously high temperature had changed the structure of bacterial community and strengthened the mainstay role of the thermophilic and spore-forming Bacillus spp. in CTC run.

Indicator organisms for assessing sanitization during composting of plant wastes

The potential for using plant pathogens and seeds as indicator organisms for assessing sanitization of plant wastes during composting was tested in bench-scale flask and large-scale systems. Plasmodiophora brassicae was unsuitable due to high temperature tolerance in dry to moist composts, and detection of viable inoculum post-composting using bioassay plants not corresponding with that using TaqMan® PCR, possibly due to preservation of nucleic acids at elevated temperatures. Several other plant pathogens (Sclerotinia sclerotiorum, Microdochium nivale, Phytophthora cinnamomi and Phytophthora nicotianae) were unsuitable due their low temperature tolerance. Fusarium oxysporum f.sp. cepae and f.sp. radicis-lycopersici chlamydospores and tomato seeds were suitable indicators due to their moderate temperature tolerance and ease of viability testing post-composting. Abutilon seeds were more tolerant than tomato seeds of compost temperatures ≥52°C but more prone to degradation at lower temperatures and therefore less suitable as indicators. Relationships between compost temperature during exposures of 2-10 days and subsequent viability of the above chlamydospores or seeds enabled the sanitizing effect of composting processes to be predicted within 2-6 days. Plant waste type (woody or vegetable) had a small but significant effect on the relationship for tomato seeds but not for F. oxysporum chlamydospores.